This disclosure pertains to artificial nucleic acids and, more particularly, to artificial nucleic acid backbones which do not hybridize well to DNA or RNA, as well as their production and uses, including for diagnostic and chemotherapeutic purposes.
For about the last 20 years, a number of nucleic acid analogues have been synthesized to modify or improve nucleic acid hybridization characteristics. The properties of the nucleic acid analogues can be classified as those which hybridize to natural nucleic acids and those that hybridize only to themselves and not to natural nucleic acids. Peptide nucleic acids exhibit strong hybridization with DNA and RNA (Nielsen et al, Science 254: 1497-1500 (1991) and similarly locked nucleic acids show increased stability and discrimination properties when hybridized to nucleic acids (Koshkin et al, Tetrahedron 54: 3607-3630 (1998)). Other nucleic acid analogues with DNA and RNA binding properties include pyrrolidinyl peptide nucleic acid (Vilaivan et al, Artificial DNA; PNA & XNA, 2: 50-59 (2011)).
Pyranosyl nucleic acid (p-RNA), and 3-deoxypyranosyl nucleic acid (p-DNA) are polymers that preferentially pair with complementary pRNA or pDNA versus natural DNA and RNA sequences (Schlonvogt et al. Helv. Chim. Acta 79, 2316 (1996), Ashkerman et al. Helv. Chim., Acta 85, 1443-1462 (2002)). Pentopyranosyl nucleic acid preparation and use for the production of a therapeutic, diagnostic and/or electronic component has been described (U.S. Pat. No. 6,506,896, U.S. Pat. No. 7,153,955).
Acyclic phosphodiester nucleic acid backbones have been disclosed, for example, for GNA (Zang et al.), aTNA (Asanuma et al., J. Am Chem Soc., 132: 14702-14703 (2010) and UNA (Peterson et al., Organic & Biomolecular Chemistry, 9(10):3591-3597 (2011). The (R)- and (S)-enantiomers of glycol nucleic acid (GNA) do not cross-pair with each other or with DNA: however. (S)-GNA cross-pairs with RNA (Johnson et al., J. Org. Chem., 76:7964-74 (2011): Zhang et al., J. Amer. Chem. Soc, 127: 4174-4175 (2005)). Benzene-phosphate backbone (Ueno et al., Nucl. Acids Symposium Series., 51: 293-294 (2007)) is another preferably self-hybridizing backbone. A number of purine and pyrimidine acyclic nucleosides were disclosed and tested as antivirals (Guillarme et al., Tetrahedron, 59: 2177-2184(2003)).
Depurination is the cleavage of the glycosidic bond connecting the purine base to sugar during oligonucleotides synthesis and during the synthesis of the purine phosphoramidites. Limitation of depurination requires special protecting groups and reaction conditions (Froehler and Matteucci. Nucl. Acids Res., 11: 8031-8036 (1983). McBride et al., J. Amer. Chem. Soc., 108: 2040-2048 (1986)). For these reasons, it is therefore desirable to utilize artificial nucleic acids that lack the glycosidic bond.
The design of multiple nucleic acid sequences with the same Tm poses special challenges for use in applications such as microarrays and nano-fabrications. It is essential to prevent undesired hybridizations. It is also required that multiple nucleic acid sequences need to be designed that do not hybridize non-specifically with each other (Tanaka et al., Nucl. Acids. Res., 33: 903-911(2005)). These so-called orthogonal nucleic acids can be designed as described in U.S. Application Publication No. 2012/0015358. The orthogonal nucleic acids with low affinity for DNA or/and not recognizable by DNA processing enzymes can be especially useful for labeling, barcoding or anchoring of multiple DNA-containing substrates co-existing in one mixture or on one array.